If Lou doesn't give you Post of the Month for that, he needs to be fired.

PS: The scare quotes around 'Doc'? The perfect touch!

I haven't made a POTM graphic. Will that hold you over?

I guess it will have to do. :angry:

Id like to thank all the little people that made this possible. Finally my jelousy-ridden peers have aknolejedaknowliged seen my geniuseness and awarded me that which has alluded such lunimaries as John A. Davidson, Larry Farfleman, Louis and even that so-called Newton of Informations, William Dembski.

I stand before you even grander than before and a giant among pigmies. You may bask in my radiunce. But this thread is not about me, it is about Lou. (HAHAHA! I WIN!!!1!1)

--------------"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

My notes and thoughts from Biology 111, for Monday, August 25, 2008. The entire series can be found here in blog post form. To go to this post directly, click here.

We began Monday's lecture where we left off on Friday (which is always a good place to start). Doc put the tree of life back up on the white board, and we did a quick review of what we went over on Friday regarding inheritance and emergence.

We then began to work a bit on Natural Selection, using Salmon as an example.

Doc stressed that Natural Selection works at the Population level, and not at the individual level. It's important to stress this, as it's the beginning of the explanation of why dogs don't give birth to cats, that tired old moronic Creationist standby.

Salmon

We talked about the life cycle of the salmon. Salmon breed and spawn up river, in fresh-water lakes. The young remain in the lake until they are ready, then swim downstream to the ocean. Once out on the ocean, they mature. When they are ready to breed, they return up the same river in which they were born, spawning in the same waters as their parents did.

There is a natural variation in the body size of adult salmon. Remember We're talking about adult salmon size, not babies. That becomes important in a moment.

This is a gill net. It is the tool used by commercial fishermen to catch salmon. Of course, the fishermen want to catch the largest fish, to maximize the price they get per fish. To accomplish this, the net is sized with large holes between the strands, so that smaller fish get through.

The way a gill net works is that as the fish swim through, the large ones get partially through, then can go no further. In an attempt to escape, the salmon back up. At that point, their gills get caught in the net.

So what happens is that in a river fished with commercial gill nets, the smaller fish have a selective advantage, and live to breed another season. This imparts a genetic tendency toward smaller size salmon, as smaller salmon tend to have smaller offspring.

In a river not fished with commercial gill nets, the larger fish have a selective advantage, as they outsize a certain proportion of their natural predators. The predators pick off the smaller fish, and that population of salmon will tend to have larger offspring. The larger fish have a smaller pool of predators large enough to eat them, so the larger salmon have an advantage here, and tend to live longer - long enough to breed. It's good to be bigger than the guy who wants to eat you.

Looking back at the tree of life chart, one population can be said to acquire trait Q, a smaller size, and the other population trait X, a larger size. As other changes take place due to other selective pressures that differ in the two populations of salmon, there may come a speciation event.

Again, speciation does not occur at the individual organism level, but at the population level. Descent with Modification is an emergent property at the population level.

Chapter Two - The Chemical Context of Life

This was pretty basic chemistry stuff.

There are 92 naturally occurring elements ---&gt; about a dozen are important to biology

Electrical attraction stablizes orbits, as the protons and electrons attract one another due to opposite electrical charges, but protons will repel each other and electrons will repel each other due to same electrical charges. Bear in mind that sketch is not to scale.

Note the protons and neutrons clustered in the nucleus, which gives the nucleus a positive charge.

Lab notes will have to wait, as I have Spanish and Precalc homework that needs attention. (Preview hint: we got to play with live termites!)

*Individuals with certain traits produce more offspring than those with other traits.

** The unit of mass for subatomic particles is the Dalton (also sometimes known as the Atomic Mass Unit or AMU), named for John Dalton, the modern developer of Atomic Theory.

So what happens is that in a river fished with commercial gill nets, the smaller fish have a selective advantage, and live to breed another season. This imparts a genetic tendency toward smaller size salmon, as smaller salmon tend to have smaller offspring.

Iteroparous species breed multiple times over a lifetime. Semelparous species breed once in a lifetime.

The negative selective effect described for gill nets will be stronger for semelparous rather than iteroparous species. IIRC, the explanation hinges on the age-specific distribution of V_x, "reproductive value". Depending on that distribution and the specifics of the heritability of size at a given age, it could actually be the case that positive selection for the trait would be favored in an iteroparous population despite universal exposure to gill-nets. Essentially, if the selective disadvantage in loss of V_x at the oldest age classes is more than balanced by increased V_x in the younger age classes, positive selection for the trait will continue.

Consequence: the example is undercut by describing its application to iteroparous species. The example should, for pedagogical purposes, refer only to the case for semelparous species.

A similar argument as what I outlined above underlies Medawar's hypothesis of senescence.

My notes and thoughts from Biology 111, for Monday, August 25, 2008. The entire series can be found here.

Lab on Monday was another really fascinating demonstration of the Scientific Method. We even got to play with real live bugs - termites, to be specific. The college keeps a colony of them, which is just cool in and of itself.

So the lab opened with Doc having us split into groups of three and four again, and then handed out a blank sheet of white paper to each group, along with a red ball-point pen and a small paint brush. Each group was instructed to make a circle on the paper using the red pen.

Then the fun part started.

Doc walked around to each group with a little tupperware container, beginning with our group. When she saw what he had in the tupperware, my female lab parter immediately got a little squicked out. Termites!

Just seeing her squirm was worth the price of admission, but by the end of the lab she was fine, as long as she didn't have to touch them with her hand. Fortunately for her, that's what the paintbrush was for. Once the termite was on the paper, the paintbrush was for wrangling the termite without squishing him. All we had to do was make sure he didn't wander off the paper.

So I had the paintbrush, because Squicky Britches was still icking out, and all of a sudden, something totally unexpected happened.

Our little termite had begun to follow the red line in a circle! He was like a little NASCAR driver, in a continuous left turn.

We started hollering at the other groups, telling them all about how brilliant our little termite (who I'd named Fred) was. About that time, other groups were still receiving their termites, and everyone was standing or craning to check out our little prodigy.

Then one at a time, other termites began to find the red circles, and sure enough, they started racing around their own little tracks.

Doc let us just be fascinated for a while, which was way cool of him. I don't think anyone in the room was anything short of amazed at this behavior. Eventually though, it was time to get to work. What was causing this behavior in the termites? Our mission, whether we chose to accept it or not, was to figure it out.

Observation:

Given a white sheet of paper with a red circle in ball-point ink and a live termite, the termite tends to follow the red line. A second termite (who we named Ginger, though my lab partners are much too young to understand the significance) exhibits the same behavior.

Question:

What causes the termites to tend to follow the red line?

Hypotheses:

We formed four hypotheses in the beginning, the testing of which is the focus of this lab.

Hypothesis #1) The termite prefers to travel in a circle.

Hypothesis #2) The termite is attracted to the color red.

Hypothesis #3) The termite is attracted to a chemical in the ink.

Hypothesis #4) The termite is following the indentation in the paper made by the pressure of the pen.

Testing Hypothesis #1

Prediction: Using the original red ink pen, a square is drawn, and if the termite simply prefers to travel in circles, then it will not follow the square.

Observation: The termite follows the square, though it has a little trouble with the corners at first.

Conclusion: The termite does not simply prefer to travel in a circle, and the hypothesis is falsified.

Testing Hypothesis #2

Prediction: Using a black ball-point pen, a circle is drawn and if the termite is attracted to the color red, then it will not follow the black circle.

Observation: The termite follows the black circle even better than it follows the red circle.

Conclusion: The termite is not simply attracted to the color red, and the hypothesis is falsified.

Testing Hypothesis #3

Prediction: Using a colored pencil, a circle is drawn and if the termite is attracted to a chemical in the ball-point ink, then it will not follow the circle.

Observation: The termite does not follow the circle at all, and basically ignores the circle completely, crossing its path many times.

Conclusion: The termite might be attracted to a chemical in the ball-point ink that is not present in a colored pencil, and the hypothesis is supported by the evidence.

Testing Hypothesis #4

Prediction: Using the tip of a pen cap, a circle is drawn without making a visible mark, and if the termite does not follow the circle, then it is not simply following the indentation in the paper made by the pressure of the pen.

Observation: The termite does not follow the circle at all, and basically ignores the circle completely, crossing its path many times.

Conclusion: The termite is not simply following the indentation in the paper made by the pressure of the pen, and the hypothesis is falsified.

At this point, we were fairly confident that we were on the right track. It was time for our break, so Doc passed out little covered petri dishes to each group with pieces of wet paper towels in them. We put Fred and Ginger into our dish, and went for our break. Fred was not looking very good at this point, and seemed to need a rest from all that racing around he'd been doing, so the timing worked out pretty well.

While on break, it occurred to us that we might want to find out exactly what it was in the ink that termites found attractive, but one of the rules to the lab was that we could use anything in the room to test our hypotheses, but nothing else.

Upon returning from break, we asked Doc if we might have another termite, as Fred was looking rather peaked. He happily obliged us, and we tested various other writing implements to observe the behavior of our new termite. Our new termite really zipped around the circle made by Squicky Britches' black bic pen, so we named him Speedy.

It then occurred to us to check another black ball-point, to see if there might be some inks the termites preferred over others. Sure enough, Speedy showed a definite preference for Squicky Britches' bic over my zebra.

Thinking about the ink and the petri dishes, we wondered if the attractive chemical might be just moisture, plain old H2O in the ink.

Hypothesis #5) The termite is attracted to the moisture content of the ball-point ink.

Testing Hypothesis #5

Prediction: Using the tip of a mechanical pencil dipped in bottled water, a circle is drawn, and if the termite does not follow the circle, it is not simply attracted to the moisture content of the ball-point ink.

Observation: The termite does not follow the circle at all, and actually seems to avoid the dampness left on the paper.

Conclusion: The termite is not simply attracted to the moisture content of the ball-point ink, and the hypothesis is falsified.

We talked a bit with Doc about our experiment to this point, and he reminded us that we were allowed to use anything in the lab to test our hypothesis further. Looking around, Squicky Britches (who was so wrapped up in termite wrangling at this point that she wasn't squicky at all) noticed the transparency papers that Doc had lying on the other end of the lab table. As a control measure, we drew a fresh circle on fresh paper with Squicky Britches' bic, and retested Speedy on that circle. As expected, he followed the circle without a problem.

Further testing of Hypothesis #3

Prediction: When a circle is drawn and the termite is separated from the paper by a transparency film, if the termite follows the circle, then it is not simply attracted to a chemical in the ball-point ink.

Observation: After anthor control in which the termite followed a fresh circle directly on a fresh paper, the termite did not follow the same circle when separated from the paper by a sheet of transparency film.

Conclusion: The termite might be attracted to a chemical in the ball-point ink, and the hypothesis is still supported by the evidence.

So this was another really fun lab for us to practice our Scientific Method skills. Sadly, I don't think Fred survived it.

So this was another really fun lab for us to practice our Scientific Method skills. Sadly, I don't think Fred survived it.

Crap. I just wrote a $300 check for my annual termite contract and all I needed to do was draw a ballpoint pen line from my house down to the road.

--------------It's natural to be curious about our world, but the scientific method is just one theory about how to best understand it. We live in a democracy, which means we should treat every theory equally. - Steven Colbert, I Am America (and So Can You!)

Outstanding series of posts. I haven't taken any regular biology classes since HS (physics major.)

One other test I thought of for your termites might have been:

Hypothesis: Is it the ink alone or an interaction with the ink and the paper.

Prediction: It is the ink alone. Mark out a new circle with the best ink (Squitchy Britches black pen) on the transparency film or on a clean sheet of frosted glass (so the ink will actually adhere.) See if the termite follows the ink.

Thanks again for a great series of posts. I will be watching this thread regularly.

-DU-

--------------Being laughed at doesn't mean you're progressing along some line. It probably just means you're saying some stupid shit -stevestory

Outstanding series of posts. I haven't taken any regular biology classes since HS (physics major.)

One other test I thought of for your termites might have been:

Hypothesis: Is it the ink alone or an interaction with the ink and the paper.

Prediction: It is the ink alone. Mark out a new circle with the best ink (Squitchy Britches black pen) on the transparency film or on a clean sheet of frosted glass (so the ink will actually adhere.) See if the termite follows the ink.

Thanks again for a great series of posts. I will be watching this thread regularly.

-DU-

Thanks DU. I'm still working on yesterday's lecture notes, and of course I have the lecture again tomorrow morning...

Hopefully, I'll get caught up by Saturday sometime.

Squicky Britches actually did try writing on the transparency, just as we were supposed to return Fred, Ginger, and Speedy to Doc. (Somehow, there must be a Snow White joke in there somewhere...) She couldn't get the ink to stick though, so we let it go.

Glad you're reading.

Quote (bystander @ Aug. 28 2008,21:46)

Leave us hanging!! I wants to know the answer

You left out disembodied telic entity pushing the termites around using wormholes in the space time continum.

Which is the correct answer no matter what your mere evidence shows. Teach the controversy !1!!one!!

Yeah, so do we. Nature never told us the answer, and neither did Doc. We're pretty confident in our hypothesis, given the evidence we have in hand.

Of course, a week from Monday, new evidence may come in and refute our hypothesis, in which case we'll look at whether we have to make some adjustments or if we have to scrap it altogether and start down another path.

As my Pop always says, "Some days'll be like that."

For the moment though, we have no evidence of disembodied telic entities, ghosts, or leprechauns pushing the termites around. We're sticking with the substance in the ink hypothesis for the moment.

--------------Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecatedI think I might love you. Don't tell Deadman -Wolfhound

For the moment though, we have no evidence of disembodied telic entities, ghosts, or leprechauns pushing the termites around. We're sticking with the substance in the ink hypothesis for the moment.

:)

Maybe you should check for quantum coherence in their microtubules. I'm sure TP can help you with experimental design. :D

Dang it, I was going to suggest the same thing. You gotta be quick here!

Interestingly, the bacterial symbionts in termite guts were the first case where tubulin (and microtubules) were found in prokaryotes. Here's an old reference from Science. This is one of the bits of evidence for Margulis's endosymbiont hypothesis; cilia and flagella might have arisen from prokaryotic endosymbionts that were like modern spirochetes.

Perhaps TP can tell us if the prokaryotic microtubules and the termite microtubules exhibit quantum properties...

--------------Flesh of the sky, child of the sky, the mindHas been obligated from the beginningTo create an ordered universeAs the only possible proof of its own inheritance. - Pattiann Rogers

For the moment though, we have no evidence of disembodied telic entities, ghosts, or leprechauns pushing the termites around. We're sticking with the substance in the ink hypothesis for the moment.

:)

Maybe you should check for quantum coherence in their microtubules. I'm sure TP can help you with experimental design. :D

Dang it, I was going to suggest the same thing. You gotta be quick here!

Interestingly, the bacterial symbionts in termite guts were the first case where tubulin (and microtubules) were found in prokaryotes. Here's an old reference from Science. This is one of the bits of evidence for Margulis's endosymbiont hypothesis; cilia and flagella might have arisen from prokaryotic endosymbionts that were like modern spirochetes.

Perhaps TP can tell us if the prokaryotic microtubules and the termite microtubules exhibit quantum properties...

Yeah, I learned way too much about termite guts reading Margulis' Symbiosis in Cell Evolution but the tubulin hypothesis never caught on the way mitochodria and chloroplasts did. Now if flagella had their own DNA...

As to learning tips. I have not heard he writeup one before but it sounds damned good. Here is one I came to late in life: Pre-read lessons, highlight what you do not understand. If you still do not understand when it is covered in class, ask questions until you do.

For me: I find it hard just to remember facts (but I am sure the re-writing would help), if I understand the process I tend to remember better.

My notes and thoughts from Biology 111, for Wednesday, August 27, 2008. The entire series can be found here.

Wednesday's lecture began with a review of atomic structure, including a reminder that our e- * diagrams are 2D representations of 3D space.

Then we moved on to some more basic chemistry.

We focused mostly on electrons, and will continue to, as electrons are what determines reactivity of an atom, and reactivity is what's really vital to biology.

e- orbits are called e- shells or energy levels. Each e- orbital can hold up to 2 e-.

The first energy level has one orbital, because it's so small, and electrons, having all the same negative electrical charge, repel each other.

The second and third energy levels each contain 4 orbitals, each energy level then is capable of holding 8 e- (2 e- in each orbital).

Then doc talked about how electrons fill from the innermost energy level, out.

e- contain Potential Energy due to location or structure.

Potential Energy is energy stored up that can be used to do work. For instance, because our lecture room is on the second floor, I have more potential energy than the student just below me on the first floor. Should a hole open up under my seat, I would fall down, releasing that potential energy as kinetic energy. That energy would be doing work, like breaking the table below me, breaking my bones, or with a water wheel type contraption the energy released by my falling could be used to produce electricity.

Now, in order to get that potential energy, I had to walk up the steps, doing work, trading kinetic energy for potential energy. So to get energy out, I first had to put energy in.

Remembering that the potential energy in my body on the second floor is caused by my distance from the center of gravity of the planet, likewise the potential energy of an electron is caused by its distance from the nucleus of an atom (though the force involved here would be electromagnetism rather than gravity). The further from the nucleus an e- is, the more potential energy it has.

e- must be in an orbital. They don't free range within the atom, and they tend towards the lowest energy level in which they can squeeze. Changing orbitals requires a change in energy. Energy into an electron causes the electron to move into higher energy levels, and energy released from an electron causes the electron to move to lower energy levels. This is often denoted by ?E, pronounced "delta E".

Doc used the example of sugar. Where does the energy we get from sugar come from? Ultimately, the sun imparts the energy to the plant via the leaves. Sunlight strikes the leaves of the sugarcane plant causing an excitement of electrons, and the plant stores that energy as potential energy. When we eat the sugar, our bodies change that back into kinetic energy, giving us a sugar rush. Thus in the end, we are eating sunlight.

So before we go any further with the notes, let's take a look at the elements we're discussing. In biology, most of the elements we're going discuss are going to be found within the first 18 elements on the periodic table. Let's have the standard periodic table, with those elements highlighted. (The original table here is from the National Institute of Standards and Technology, NIST. The electron distribution table is from a scan of page 36 in our textbook. I have put the two images together to help visualize the sections of the periodic table that we'll be discussing.)

Next up, we talked about orbitals, arrangement of electrons in those orbitals at different energy levels, and the notation we use to describe all that. The remainder of this discussion will reference this electron distribution diagram, found on page 36 of our textbook (at my blog, you can click for a larger version, hosted at my Flickr account):

Let's look now at a few elements on this chart. The obvious place to start is at the beginning, so we'll start with Hydrogen.

In this image, I've highlighted Hydrogen (H). A hydrogen atom consists of one e- and one p+. There are no neutrons in the nucleus of a stable hydrogen atom. The single electron travels in the orbit described. For our purposes, we're going to ignore the nucleus for the time being. In this notation, we're mostly concerned with electrons and their orbits.

Comparing that to Helium (He), we see that in this notation, we're not going to separate the electrons on opposite sides of the atom as they physically would tend to be, we're just noting that there are two e- in this orbit. Atoms in the same row on the periodic table have the same number of shells, and in the first electron shell, there is one orbit. Each orbit will hold up to two e-. It's easy to think of this first shell as being so small that the charge of the e- (which repel each other) are just so close that they won't allow any more electrons in the vicinity.

Further out, in larger shells, each shell will consist of four orbits, but again, each orbit can only hold 2 e-. The outer e- shell of a given atom is referred to as the valence shell. The number of e- in the valence shell is of utmost importance to chemical reactions, and thus to biology.

In the second row then, we would expect to find two e- shells, and indeed, here is Lithium (Li). Notice that Li has the inner shell full (2 e-) and then begins to work on the next shell, with its third e-. Electrons always fill out the shells from the inside out, from closest to the nucleus, to furthest from the nucleus.

Remember that except for the innermost one, e- shells each contain four e- orbits, and each orbit holds two e-. Now, each of those orbits in a shell will take on e- before any of them will take a second e-. Thus the notation for Beryllium shows a second electron in the valence shell, but in a separate orbit from the first e-.

Boron (B) takes a third e-, in a third orbit of the second shell, and then we come to Carbon ( C ). Carbon has four valence e-, one in each orbit of the valence shell. Each of the four e- orbits of the valence shell now has a single electron.

The next element, Nitrogen (N), has five valence e-, and the fifth one can now go in the first orbit of the valence shell, since each orbit in the shell now has one electron.

Predictably, Oxygen then takes a sixth e- in the valence shell (for a total of 8 e-) and it goes in the second orbit.

At this point a patterns should be emerging. Notice that in the first column, all the elements have one valence e-, in the second they all have two, etc.

In the eighth column, all the elements have 8 valence e- (except He), meaning that their valence shells are full. The elements in this column are referred to as the Noble Gases, or the Inert Gases. Elements with full valence shells are non-reactive. They are happy with the number of e- they have, and tend not to interact with other elements.

Atoms are most stable when they have NO unpaired electrons. Natural things tend toward their most stable state. A stack of bricks is less stable than those same bricks all flat on the ground. Likewise, elements tend towards having full valence shells.

We can say then that the reactivity of an atom depends on the number of unpaired valence e-. This becomes very important for biological chemistry.

Now that we had a good idea about valence e-, we could take that information and apply it.

Chemical Bonds

We began our discussion of chemical bonds with the first type, which is called Covalent Bonding.

There are a couple ways for atoms to find e- to fill up their valence shells. They can steal one from another atom (called ionic bonding, discussed in the next lecture). But like in life, bigger atoms are better at this than small atoms. To quote Doc directly,

Quote

"If you want to be successful at taking something from someone else, you had better be bigger than them, or they will whoop your ass and take it back. Hydrogen is the smallest atom, so it will always be the whoopee, not the whooper."

So hydrogen goes a different route. It shares electrons. This is called a covalent bond.

In this fashion, two hydrogen atoms can each fill their valence shell (they each now have two e- in the valence shell). They are sharing a single pair of electrons, so this is a single bond.

We can write this in a number of ways.

There is the molecular formula

H2

The structural formula

H-H

and the Lewis Dot diagram

H:H

Oxygen, having two spots to fill in its valence shell, will share two pairs of electrons, and Nitrogen, 3. In the quick sketch I did above (forgive the lack of neatness there...), the molecular notation, the structural notation, and the Lewis Dot Diagram are given for Oxygen and Nitrogen, the two most abundant elements in the air we breathe.

The lecture ended there. On Friday, we discussed electronegativity. I'll get those notes up (hopefully) by tomorrow.

* remembering our shorthand, e- means electron, p+ is for proton, and n is for neutron.

Quote

From whence came the art:

The first image is of our textbook, Biology, Eighth Edition, by Campbell &amp; Reese et al. The electron distribution table is from page 36 of that textbook, and I have highlighted portions of it in the various images above to assist in visualization.

As to learning tips. I have not heard he writeup one before but it sounds damned good. Here is one I came to late in life: Pre-read lessons, highlight what you do not understand. If you still do not understand when it is covered in class, ask questions until you do.

For me: I find it hard just to remember facts (but I am sure the re-writing would help), if I understand the process I tend to remember better.

Thanks Stephen.

--------------Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecatedI think I might love you. Don't tell Deadman -Wolfhound

I think that your understanding of the basic material may be better than some of my students. Here is an email, rec'd tonight, from a student in my intro bio class. The name is withheld to protect the innocent...

Quote

I was reading the textbook and I am now confused.

On page 4, it defines Atoms as "...the fundamental building blocks of all substances, living and non-living."Then on page 22, it goes on to say that ... "Atoms differ in the number of subatomic particles, but all have a nucleus..."--- Back on page 8, it told me that bacteria & archaea are single-celled organisms, but that they are prokaryotic, meaning that they have no nucleus.. ..Farther back still, on page four, it says in short : atoms join together to make molecules, and molecules (become organized into?) make cells...

So as I said I am confused. Is the textbook saying that some molecules are formed without atoms? If so, what are they made of?

..Or is page 22 incorrect about all atoms having nuclei or is there something else ?

Thanks for clearing this up

--------------Flesh of the sky, child of the sky, the mindHas been obligated from the beginningTo create an ordered universeAs the only possible proof of its own inheritance. - Pattiann Rogers